Mammalian Methylation Consortium Github Page

This page contains all the annotation and tools generated by Mammalian Methylation Consortium to analyze generated data using Mammal40k and Mammal320 arrays:

Here are the summary of the content:
1- Genome coordinates for different species
2- R code for alignment and annotation
3- The array manifest
4- Details on probe design
5- R code for Sesame normalization
6- R code for universal pan-mammalian epigenetic clocks, universal blood epigenetic clocks, universal skin epigenetic clocks, adaptions to Illumina 450k/EPIC array, and an example dataset
7- Various tissue, sex, and species predictors for mammalian species
8- Codes used for Mammalian Network Analysis in the paper, Haghani et al. DNA Methylation Networks Underlying Mammalian Traits, Science Magazine, 2023.
9- EnsembleAge R Package: Complete R package for automated multi-platform epigenetic age prediction with ensemble methods (Human, Mammal40k, Mammal320k arrays). Features automatic platform detection, data preprocessing, and 110+ individual clocks including EnsembleAge Static/Dynamic, Universal clocks, and original mammalian clocks. Installation: devtools::install_github('ahaghani/EnsembleAge') - one-line prediction with predictEnsemble(data, samples). Published methodology provides enhanced accuracy through ensemble approaches combining multiple clock families for robust age predictions across species and tissues.

Key references on Mammalian Methylation Array:

Details on the array development:
Arneson, A., Haghani, A., Thompson, M. J., Pellegrini, M., Kwon, S. B., Vu, H., Maciejewski, E., Yao, M., Li, C. Z., Lu, A. T., Morselli, M., Rubbi, L., Barnes, B., Hansen, K. D., Zhou, W., Breeze, C. E., Ernst, J., & Horvath, S. (2022). A mammalian methylation array for profiling methylation levels at conserved sequences. Nat Commun, 13(1), 783. https://doi.org/10.1038/s41467-022-28355-z

Mammalian Methylation Dataset and a cross species meta analysis:
Haghani, A., Li, C. Z., Robeck, T. R., Zhang, J., Lu, A. T., Ablaeva, J., Acosta-Rodriguez, V. A., Adams, D. M., Alagaili, A. N., Almunia, J., Aloysius, A., Amor, N. M. S., Ardehali, R., Arneson, A., Baker, C. S., Banks, G., Belov, K., Bennett, N. C., Black, P., . . . Horvath, S. (2023). DNA methylation networks underlying mammalian traits. Science, 381(6658), eabq5693. https://doi.org/10.1126/science.abq5693

A paper on the universal epigenetic clocks in mammals:
Lu, A. T., Fei, Z., Haghani, A., Robeck, T. R., Zoller, J. A., Li, C. Z., Lowe, R., Yan, Q., Zhang, J., Vu, H., Ablaeva, J., Acosta-Rodriguez, V. A., Adams, D. M., Almunia, J., Aloysius, A., Ardehali, R., Arneson, A., Baker, C. S., Banks, G., . . . Horvath, S. (2023). Universal DNA methylation age across mammalian tissues. Nat Aging. https://doi.org/10.1038/s43587-023-00462-6

EnsembleAge package for multi-platform epigenetic age prediction:
Haghani, A., Lu, A.T., Yan, Q. et al. EnsembleAge: enhancing epigenetic age assessment with a multi-clock framework. GeroScience (2025). DOI: 10.1007/s11357-025-01808-1

EnsembleAge R Package

Latest Addition: Complete R package for multi-platform epigenetic age prediction using ensemble methods.

• Repository: EnsembleAge
• Installation: devtools::install_github('ahaghani/EnsembleAge', ref='v0.99.1')
• Platforms: Human, Mammal40k, Mammal320k arrays (automatic detection)
• Publication: Haghani, A., Lu, A.T., Yan, Q. et al. EnsembleAge: enhancing epigenetic age assessment with a multi-clock framework. GeroScience (2025). DOI: 10.1007/s11357-025-01808-1
• Release DOI: